Re: [OBO-Edit Working Group] bringing back to live obslolete terms

[Karen C. <kc...@ge...>]

Hi,

I agree with you John that I would be very hesitant to add the ability to
un-obsolete terms. Terms have generally been obsoleted for good reasons.
As the GOid actually goes with the definition, not with the string of the
term name, if you do need to add a term with a name that is identical to
the name of a term that has been obsoleted, you would have to use a new
GOid unless the definition of the new term is identical to that of the one
that has been obsoleted. I think it is very unlikely that people would
want to reinstate obsoleted terms with the same definition as the
obsoleted term.

-Karen


On Thu, 26 Jan 2006, John Day-Richter wrote:

> Shuly Avraham wrote:
> 
> > Hi John,
> >
> > At the POC, we would like to have the option of bringing back to  
> > live' obslolete terms in DAG-editor, by simply moving an obsolete  
> > term back to the ontology. This cannot be done in DAG-editor (OBO- 
> > editor might allow that?).
> >
> > We recently realized we need the term 'organ' which was obsoleted  
> > before, but we'd rather not to add new term 'organ' in order to avoid  
> > having two identical terms (though with different IDs) in the same  
> > ontology, one in obsolete node, another one under 'plant structure'.
> >
> > Can that be a feature request?
> 
> I'm very hesitant to add this feature.
> 
> It's technically very simple to do. The code to do it is actually 
> already written, and is called when you use undo to reverse an obsoletion.
> 
> However, unobsolete has the potential for disastrous consequences in 
> published ontologies. Normally, if a term is obsoleted, there was some 
> problem with it, or confusion about its meaning. Even if you decide 
> later you want to use the term, it's VERY unlikely that you mean to use 
> the term *with the exact same meaning as before*. And if the meaning has 
> changed, you need to create a new term with a new id. Plus, most 
> programs that use OBO ontologies are written with the assumption that 
> obsolete terms never come back to life; who knows what would happen to 
> the Yeast database, for example, if a once obsolete term suddenly 
> reappeared in the ontology?
> 
> I'd like to hear from some other people on whether we think its a good 
> idea to have this feature. I'm in favor of creating a new term with a 
> new id. It's no big deal if there are multiple terms with the same name, 
> particularly if only one of those terms is non-obsolete.
> 
> If I did add this feature, it would certainly come with an elaborate 
> warning like: "You are probably making a mistake! In 99.9% of cases, you 
> should just create a new term instead of unobsoleting. Are you 
> absolutely sure this is what you want to do?"
> 
>     -John
> 
> 
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